I'm in Japan, Kansai area. I find advanced brewing a bit expensive but they have a pretty good assortment. You could try sakeland.net as well. Assortment is less but prices more friendly. I mostly order from them.
Advanced brewing and sakeland are both pretty good. If you want to give some business to a great guy, a fellow foreigner/brewer who's started his own brewing supplies business then have a look at the link below. He goes by the name of Tektonjp on HBT. I just got my first shipment, ordered two days ago and arrived at my door, this morning. Great service.
Also, if you can use and store grains in bulk, 20 kg sacks are very reasonably priced at Asahi malts, based in Shiga prefecture, I believe. Last time I bought from them was about three years ago and they cost about ¥3,800 each plus ¥600 per sack for transportation, this was a German Pilsener malt and an English Pale Ale malt. They had a decent selection, from what I remember.
I'm moving from London to Tokyo in May and have been checking the availability of homebrew supplies in Japan. Things have definitely improved compared to the last time I lived in Japan. But yikes, hops are expensive. Maybe I'll make a bulk purchase and bring it all with me (although now I imagine getting stopped at customs at Haneda with 100kg of hops....)